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The commands choose $n=100$ observations and $p=2$ predictors; generate a $100\times 2$ matrix $X$ of independent standard-normal values; generate independent binary random variables $Y_i$ with success probability $1/2$; and report the observed number of successes, ${\sum }_i{Y}_i=48$. The first glm call then fits the Bernoulli logistic-regression modelThe prediction command returns the fitted response probabilities ${\hat{p}}_i$ and sums them.

The likelihood isAt the maximum-likelihood estimator, the intercept component of the score function isThereforeexactly, by the fitted-mean balance for logistic regression with an intercept.

The second fit uses probit regression,where $\Phi$ is the standard normal distribution function. Its intercept score isa weighted residual equation. It does not imply ${\sum }_i{\hat{p}}_i=48$, so exact equality is not expected. The output should nevertheless be close to $48$: the data were generated with constant success probability $1/2$ independently of $X$, so the fitted slopes should be small, the linear predictors should cluster near a common intercept, and the score weights should be nearly constant.